CAGE-Seq Pipeline

This CAGE-seq pipeline includes rRNA filtering, Genome Alignment using STAR, and peak calling using MACS2.

This pipeline is implemented to process CAGE-seq reads reported in: Paper

Steps:

1. STAR is used to count or filter out common RNAs (eg. rRNA, miRNA, tRNA, piRNA etc.).
2. STAR is used to align RNA-Seq reads to a genome.
3. MACS2 is used for calling peaks in aligned bam files.

Program Versions:

• Star v2.6.1 # don't upgrade me - 2.7X indices incompatible with iGenomes.
• Samtools v1.3
• Bowtie2 v2.3.5
• Bowtie v1.2.2
• Bedtools v2.29.2
• Ucsc-wigToBigWig v377
• Macs2 v2.1.2

Pipeline Container:

• Docker: dolphinnext/cageseq_pipeline:1.0
• GitHub: dolphinnext/cageseq_pipeline